OTTAWA - Officers of the Canadian Security Intelligence Service have played a crucial and long-standing role as interrogators of a vast swath of captured Taliban fighters, The Canadian Press has learned.

The spies began working side-by-side with a unit of military police intelligence officers as the Afghan war spiralled out of control in 2006, according to heavily censored witness transcripts filed with the Military Police Complaints Commission.

The spy agency's previously unknown role in questioning detainees adds a new dimension to the controversy about the handling and possible torture of prisoners by Afghan security forces.

It also raises more questions about the critical early years in Kandahar when the Canadian military found itself mired in a guerrilla war it had not expected to fight.

CSIS acknowledged in 2006 that its members gathered intelligence in Afghanistan, but the spy service's precise role has remained in the shadows until now.

Maj. Kevin Rowcliffe, former staff adviser to Canada's overseas operations commander, told investigators with the complaints commission there were questions about how much experience the army's intelligence officers had in grilling prisoners.

"There was a lot of discussion in my headquarters about who was qualified to do interrogations, because we're not talking the normal police interview, we're talking interrogations, which (censored) were doing, not (military police)," says an edited transcript of the Dec. 6, 2007, interview.

A copy of the document was obtained by The Canadian Press.

Military police "were involved in that, but they weren't necessarily involved in interviewing or interrogation related issues; that would be (censored) or some other parade that had special training in interrogation."

Sources familiar with the unedited version say the blanked out references are to CSIS.

Intelligence expert Wesley Wark says the revelations are disturbing, partly because CSIS would have had no specialized knowledge of how to elicit information from Afghan prisoners.

"I find that stunning," said Wark, a historian at the University of Toronto.

But Defence Minister Peter MacKay said the threat to Canadian troops in Kandahar has been severe.

"Clearly it's in all our interest to have accurate information as we attempt to protect people," MacKay said late Sunday as he arrived in Haiti to visit Canadian troops conducting the earthquake relief mission there.

With all of the roadside bombings "the effort obviously to protect people - to protect the area around Kandahar province, which is our primary responsibility - does require intelligence and information-gathering."

MacKay acknowledged the military has "relied heavily on other departments, including CSIS."

The spy agency is legally permitted to gather intelligence anywhere in the world concerning threats to the security of Canada, and has increasingly operated abroad in recent years.

In Kandahar, CSIS officers conducted what's known as tactical field questioning, essentially the first interrogations of suspects, said another source familiar with the process.

They tried to sort out who was a bona fide insurgent commander -- or a simple field soldier.

The spies would sometimes make recommendations on which Taliban prisoners to hand over to the National Directorate of Security, Afghanistan's notorious intelligence service, the sources said.

The final say on whether to transfer always rested with the military task force commander.

MacKay said Afghan officials and NATO were kept in the loop.

"We also, of course, exchange information with our international partners which is, obviously, a subject of some controversy back home, as you know," he said.

The Military Police Complaints Commission asked questions about the CSIS role in Kandahar, but abandoned the angle when it became bogged down in legal challenges about its authority to investigate Ottawa's overall prisoner transfer policy.

Diplomat-whistleblower Richard Colvin testified before a special House of Commons committee last November that the majority of prisoners Canada handed over to the Afghan intelligence service were tortured -- a claim the Conservative government and military commanders, past and present, angrily denied.

Rowcliffe's interview transcript prompts questions about whether the military and CSIS officers had enough time to conduct proper interrogations early in the war, when newly arrived troops had little intelligence on the threats they were facing.

The military has 96 hours after capture to decided whether to hand over a prisoner to Afghan authorities, but Rowcliffe said there was pressure to turn them over sooner.

He said he took up the concerns with the commander of overseas operations, saying: "I understand the time sensitiveness of this issue to the Government of Canada, but we may have Osama bin Laden, yet you are trying to get me to give him over as quickly as possible."

But the answer was often "no." His boss, Lt.-Gen. Michel Gauthier, indicated his hands were tied and told Rowcliffe that the federal government's policy was firm.

Yet the concerns persisted.

"I said, we need to take the time to do a proper investigation, interview, interrogation, whatever you want to call it to confirm who we have and what has this guy done or gal done," Rowcliffe said in his statement.

He was asked by police commission investigators where he thought the intelligence would come from if the instructions were to get rid of detainees right away.

"My impression was they didn't seem to care about that," said Rowcliffe, who's retired from the military.

"I don't know if they didn't grasp the importance of it, or just that it was not important because the pressure was . . . to get rid of them because of the Government of Canada."

He said he wasn't sure whether there was pressure from the defence minister and the chief of defence staff.

"I have no idea, but I know from Gen. Gauthier's position that (it was): Get rid of them as quickly as you can and what's taking so long? That's the kind of questions I'd get."

Security expert Wark said it begs the question why Ottawa was so eager to transfer prisoners out of the controlled confines of Kandahar Airfield, where they are brought for initial interrogation.

It will likely fuel human-rights groups' fears that interrogation was being outsourced to the Afghans, he said.

Canada went into Kandahar thinking the Taliban and al-Qaida were simply "a nuisance" and there was a "ferocious under-estimation" of the kind of resistance troops would face, he said.

"The military simply had no expertise. It had been decades since they had to interrogate prisoners of war," Wark added. "And if the military lacked that expertise, you can be sure, CSIS lacked it in spades."

Moreover, Wark said, some hard questions need to be asked about how much knowledge CSIS had in 2006 of Afghanistan and its complex network of competing tribes.

"The answer would be very little," he said. "They didn't have a trained body of people with the language skills, knowledge of the country, knowledge of the tribal situation, who was in charge of which warlord group, what was the nature of the Taliban. Those are all issues they had to develop an expertise on after 2006."

In response to questions, CSIS spokeswoman Isabelle Scott said the agency does not discuss operations.

"We do have a presence in Afghanistan, and we've had one for the past few years. And we continue to provide security intelligence in Afghanistan in support of the safety and security of Canadian and allied forces on the ground," Scott said.

"And we also continue to gather intelligence in Afghanistan in order to mitigate potential security threats to Canada which have a nexus on that country. However, we don't publicly discuss the specific issues linked to operational activities of the service."

The activities in Kandahar caught the attention of the spy agency's inspector general, who investigated "policy gaps and inconsistencies."

The declassified version of Eva Plunkett's 2007 certificate, a top secret report card on CSIS prepared for the public safety minister, contained no suggestion that the spy service had done anything wrong -- or illegal, for that matter.

She noted that Afghanistan was "a fundamental intelligence priority" and commended the spy service for impressive work "in an extremely challenging environment." But Plunkett warned that CSIS and National Defence lacked clear policies that would "guide future (censored) activities in this theatre."

Agreements between the spy service and military were out of date, said the annual certificate, made public in May 2008. "I do believe that those who serve in this environment deserve to be equipped with the policy framework to guide their work."

In May 2006, Jack Hooper, then CSIS deputy director of operations, said the spy service's efforts to help Canadian troops in Afghanistan were principally focused on acquiring intelligence to help soldiers defend themselves against attacks.

"This intelligence is known to have saved lives, uncovered weapons and arms caches, and disrupted planned terrorist attacks."

But he did not elaborate as to exactly how CSIS obtained the valuable information.

The Security Intelligence Review Committee, a CSIS watchdog that reports to Parliament, raised concerns about the intelligence service's interaction with detainees in foreign jurisdictions in its review of the Omar Khadr file.

It said last year that when CSIS interviewed Khadr at Guantanamo Bay in 2003, there was policy governing the spy service's investigative activities outside Canada, including operational interviews abroad.

Prior to undertaking such activities, CSIS employees were required to submit a request for approval -- to whom, exactly, remains classified.

The review committee found briefing notes that had been submitted prior to each visit to Guantanamo Bay, but these requests fell short of meeting the requirements outlined in policy.